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Wayne Manor began as the simple home of railroad financier Jerome K. Van Derm in 1855. Soon after, Van Derm had to give up the property to the brothers Solomon and Zebediah Wayne in 1858. Solomon Wayne, a judge, worked hard to preserve equality in Gotham, saying that the city should be a "fortress against vice and iniquity". Solomon expanded Wayne Manor to its present size, acting as the first Wayne to turn it into a manor. They later used it as part of the Underground Railroad, sheltering escaped slaves who fled north to Canada. According to Alfred, Wayne Manor had been home to six generations of Waynes.

Although there was a vast network of limestone caverns that ran beneath the manor, Martha Wayne filled the house with warm furnishings and flowers from the Greenhouse. Many of the antiques in the estate had been passed down through multiple generations, such as the Mahogany furniture.

The current members of the Wayne family at the time of Batman Begins were Thomas Wayne, his wife Martha, and their son, Bruce. Alfred was the family's butler, and Rachel Dawes lived on the estate with her mother, the housekeeper.

One day, while playing in the Manor's garden with Rachel Dawes, Bruce fell down the old well into the caverns below. There, he faced what would become both his greatest fear and most valuable ally: the bat. Frightened out of his wits, Bruce was comforted by his father being lowered on a rope anchored by Alfred, the two adults having been alerted to Bruce's fall by Rachel. That night, Bruce had a nightmare about the bats, causing his father to come soothe him, explaining to Bruce, "They attacked you because they were afraid of you. All creatures feel fear, especially the scary ones." It would be the last time that Thomas and Martha Wayne left the house alive.

After the murder of his parents, Bruce felt guilty beyond imagination. As he remorsefully told Alfred, "It was my fault, I made them leave the theater. If I hadn't gotten scared..." Alfred, however, comforted Bruce, telling him, "It was him, and him alone".

Wayne Manor as it appeared before it was destroyed

When Bruce returned to the manor before the hearing of Joe Chill, Alfred told him he had prepared the master bedroom, but Bruce replied that he'd rather stay in his own room. When Alfred tried explaining that this was his home, Bruce snapped angrily, "This is my father's house, and now that he's dead, it's a mausoleum! If I ever have my way, I'll tear the damn thing down, brick by brick!" Little did Bruce know that he would have that accomplished for him in the future.

When Bruce returned to Gotham after training with the League of Shadows, he was informed by Alfred that William Earle had become head of Wayne Enterprises, and had declared Bruce dead, attempting to gain control of Bruce's shares of the company's stocks. Earle had also turned the company into an arms manufacturer, accepting contracts from military projects. While reading the paper in the living room about Gotham's current state, Bruce saw a bat flying in the corner near the ceiling. It was at that moment that Bruce realized that being afraid of a bat was like being afraid of a ghost, a wraith. Gathering the proper equipment, Bruce cleared the weeds blocking the well he had fallen down as a child, and ventured into the caverns. There, he was swarmed by bats, but this time, Bruce realized there was nothing to be afraid of. Thus, the caverns below became the Batcave.

During Bruce's 30th birthday party at the manor, Bruce received an unexpected guest--Henri Ducard, his mentor in the League of Shadows revealed himself to be the true Ra's al Ghul. Faking a drunken rant to protect the guests and make them leave, Bruce was left alone with Ra's al Ghul and warriors of the League. As his men begin a fire in the manor, Ra's al Ghul explained his plan: the Scarecrow's fear toxin was made from the League's blue poppies, and using this toxin, the League would poison the entire city. The compound had already spread throughout the city via the water; all that was left was to turn it into gas by using the city's monorail train system to transport the Microwave Emitter stolen from Wayne Enterprises into Wayne Tower, the center of the water mains, covering the entire city in poison. As Bruce attempts to fight off al Ghul, Ra's warns Bruce that he failed to mind his surroundings, and a pile of burning debris falls on Bruce. Ra's al Ghul leaves Bruce to burn, with a guard making sure that none come out alive. However, ever-loyal Alfred sneaks up behind the ninja and knocks him out with a golf club, rescuing Bruce and getting them both into the secret elevator into the Batcave just in time.

After finally defeating Ra's al Ghul, Bruce and Alfred return to the ruins of the manor, with Alfred supervising construction workers. Rachel arrives at the scene, and tells Bruce that his real face is the one that criminals fear, and that the man she loved never really came back, but one day, when Batman is no longer needed, she might see him again. After Rachel leaves, Alfred tells Bruce that they might be able to "improve the foundation", meaning the South-East corner, where the Batcave is located.

Wayne Manor is still being rebuilt. As a result Bruce temporarily sets up his Batcave in a hidden bunker beneath a shipping container at Wayne Enterprises' dockyard and uses it to fight off The Joker. After he finished the Joker, Batman takes the blame for Harvey Dent's death and Commissioner Gordon names him the prime suspect for the crimes Harvey committed in order to make Harvey look like a hero. Batman then evades capture by the police for the next eight years.

Eight years after Batman retired, Wayne Manor has been rebuilt, Bruce Wayne is once again residing there, sealed off in the East wing of the mansion. Bruce had become a recluse after the chaos caused by The Joker and the death of Rachel Dawes.

During the eighth anniversary of the Dent Act, a day where they celebrate an Act which put the majority of criminals in Blackgate Prison, The Wayne Foundation hosts a charity event at the manor. Bruce watches from the manor and skips participating in the celebrations. As this is happening a maid, later to be revealed as Selina Kyle, is stealing Bruce's mother's pearl necklace from his private quarters. Bruce sneaks up behind her and confronts her, but she overpowers him and escapes with the necklace.

During an investigation of the safe, Bruce discovers that the real target was his fingerprints and not the necklace. He returns to the Batcave for the first time in years and runs an analysis, only to be confronted by Alfred who asks him to return to life.
John Blake arrives at the manor, a few days later, demanding to speak with Bruce. Blake tells him about the attack on James Gordon and reveals to him that he knows Wayne is actually Batman. He warns him about another threat known as Bane and asks him again to return as Batman.

After Bruce Wayne returns as Batman, this prompts Alfred to leave Bruce alone in the Manor to try to persuade him to stop being Batman. That same day, Wayne Enterprises went bankrupt, but Bruce was allowed to keep the Manor. That night, Miranda visited Bruce in his manor, and the two shared an intimate night. Bruce left afterwards, to don his armor and fight Bane. He would never return to Wayne Manor afterwards.

By the end of The Dark Knight Rises, after the supposed death of Bruce Wayne, Wayne Manor was deeded to the city and was transformed into an orphanage, and maintained by them on condition that it remain the children's home.